xEnrichHeatmap: Function to visualise enrichment results using heatmap

Description Usage Arguments Value Note See Also Examples

View source: R/xEnrichHeatmap.r

Description

xEnrichHeatmap is supposed to visualise enrichment results using heatmap. It returns an object of class "ggplot".

Usage

1
2
3
xEnrichHeatmap(list_eTerm, fdr.cutoff = 0.05, displayBy = c("zscore",
"fdr", "pvalue", "fc", "or"), colormap = NULL, zlim = NULL,
reorder = c("none", "row", "col", "both"))

Arguments

list_eTerm

an object of class "ls_eTerm". Alterntively, it can be a data frame having all these columns (named as 'group','ontology','name','adjp') and one of these columns ("zscore","fdr","pvalue","fc","or"). Note, the column 'fdr' can be inferred from the column 'adjp'

fdr.cutoff

FDR cutoff used to declare the significant terms. By default, it is set to 0.05

displayBy

which statistics will be used for comparison. It can be "fc" for enrichment fold change (by default), "adjp" for adjusted p value (or FDR), "pvalue" for p value, "zscore" for enrichment z-score, "or" for enrichment odd ratio

colormap

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

zlim

the minimum and maximum z values for which colors should be plotted, defaulting to the range of the -log10(FDR)

reorder

how to reorder rows and columns. It can be "none" for no reordering, "row" for reordering rows according to number of sharings (by default), "col" for reordering columns, and "both" for reordering rows and columns

Value

an object of class "ggplot"

Note

none

See Also

xHeatmap

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
## Not run: 
# Load the library
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

# provide the input Genes of interest (eg 100 randomly chosen human genes)
## load human genes
org.Hs.eg <- xRDataLoader(RData='org.Hs.eg',
RData.location=RData.location)
set.seed(825)
data <- as.character(sample(org.Hs.eg$gene_info$Symbol, 100))
data

# optionally, provide the test background (if not provided, all human genes)
#background <- as.character(org.Hs.eg$gene_info$Symbol)

# 2) Gene-based enrichment analysis using ontologies (REACTOME and GOMF)
# perform enrichment analysis
ls_eTerm <- xEnricherGenesAdv(data, ontologies=c("REACTOME","GOMF"),
RData.location=RData.location)
## heatmap plot of enrichment results
gp <- xEnrichHeatmap(ls_eTerm, fdr.cutoff=0.1, displayBy="zscore")

## End(Not run)

hfang-bristol/XGR documentation built on Dec. 9, 2018, 4:38 a.m.